PG-PuReMD: code consoliation.

PG-PuReMD/Makefile.am

PG-PuReMD/src/allocate.c

PG-PuReMD/src/charges.c

PG-PuReMD/src/charges.h

PG-PuReMD/src/cuda_allocate.cu

PG-PuReMD/src/cuda_allocate.h

PG-PuReMD/src/cuda_bond_orders.cu

PG-PuReMD/src/cuda_bonds.cu

PG-PuReMD/src/cuda_charges.cu

PG-PuReMD/src/cuda_charges.h

PG-PuReMD/src/cuda_forces.cu

PG-PuReMD/src/cuda_hydrogen_bonds.cu

PG-PuReMD/src/cuda_lin_alg.cu

PG-PuReMD/src/cuda_lin_alg.h

PG-PuReMD/src/cuda_list.cu

PG-PuReMD/src/cuda_list.h

PG-PuReMD/src/cuda_multi_body.cu

PG-PuReMD/src/cuda_neighbors.cu

PG-PuReMD/src/cuda_nonbonded.cu

PG-PuReMD/src/cuda_reduction.cu